GPU Accelerated Smith-Waterman

  • Yang Liu
  • Wayne Huang
  • John Johnson
  • Sheila Vaidya
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3994)


We present a novel hardware implementation of the double affine Smith-Waterman (DASW) algorithm, which uses dynamic programming to compare and align genomic sequences such as DNA and proteins. We implement DASW on a commodity graphics card, taking advantage of the general purpose programmability of the graphics processing unit to leverage its cheap parallel processing power. The results demonstrate that our system’s performance is competitive with current optimized software packages.


Dynamic Programming Graphic Processing Unit Texture Memory Genomic Sequence Comparison Dynamic Programming Table 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Yang Liu
    • 1
  • Wayne Huang
    • 1
    • 2
  • John Johnson
    • 1
  • Sheila Vaidya
    • 1
  1. 1.Lawrence Livermore National Laboratory 
  2. 2.DOE Joint Genome Institute, UCRL-CONF-218814 

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